Simulation of Y-chromosomal haplotype data

The non-recombining nature of the Y-chromosome determines the non-independence of alleles between loci. The evolution of short tandem repeat (STR) loci in the Y-chromosome is the result of different factors such as differential mutation rates, mutation modes, gene conversion, selection and demographic processes. The degree of correlation between loci is dependent on the magnitude of these processes. The simulation of data is a routine tool used for testing hypotheses in population and evolutionary studies. The most basic parameters hitherto used in lineage haplotype simulations are the allele frequency distributions and mutation rates, assuming either full independence or linkage between loci. In this study we introduce use of the Spearman correlation coefficient to estimate the degree of dependence between non-recombining loci. Then, both the interdependence between loci and the allele frequency distributions at multi-allelic loci are incorporated in an algorithm for simulating haplotypes. We illustrate the method using published and unpublished Y-chromosome STR data.     

HLA gene and haplotype frequencies in galicia (NW Spain)

The genetic structure of six populations of Iran (Turks, Kurds, Lurs, Zabolis, Baluchis and Zoroastrians) was examined using data on blood groups, serum proteins and cell enzymes. Our results show conclusively that there are genetic differences among the six populations and the analysis of superimposed R and S matrices defined by Harpending & Jenkins (1973) show that the dispersion of some of the alleles correspond to the dispersion of the populations. The F_ST estimates are not large enough to favour selection on any of the loci studied. The F_IT and F_IS estimates are positive and moderately high suggesting that the genetic differentiation to some extent is influenced by inbreeding.     

Genetic association between bovine NOD2 polymorphisms and infection by Mycobacterium avium subsp. paratuberculosis in Holstein‐Friesian cattle

Nucleotide‐Binding Oligomerization Domain 2 (NOD2) has been reported to be a candidate gene for Mycobacterium avium subsp. paratuberculosis (MAP) infection in a Bos taurus × Bos indicus mixed breed based on a genetic association with the c.2197T>C single nucleotide polymorphism (SNP). Nevertheless, this SNP has also been reported to be monomorphic in the B. taurus species. In the present work, 18 SNPs spanning the bovine NOD2 gene have been analysed in a genetic association study of two independent populations of Holstein‐Friesian cattle. We found that the C allele of SNP c.*1908C>T, located in the 3′‐UTR region of the gene, is significantly more frequent in infected animals than in healthy ones, which supports the idea that the bovine NOD2 gene plays a role in susceptibility to MAP infection. However, in silico analyses of the NOD2 nucleotide sequence did not yield definitive data about a possible direct effect of SNP c.*1908C>T on susceptibility to infection and led us to consider its linkage disequilibrium with the causative variant. A more exhaustive genetic association study including all putative, functional SNPs from this gene and subsequent functional analyses needs to be conducted to achieve a more complete understanding of how different variants of NOD2 may affect susceptibility to MAP infection in cattle.     

The Fat Mass and Obesity-Associated (FTO) Gene is Associated with Intramuscular Fat Content and Growth Rate in the Pig

The association of the FTO gene with obesity has been implicated in various human populations. The FTO gene is also most likely involved in the regulation of energy balance and feed intake. Here, the FTO gene was studied as a candidate gene for fatness and growth rate traits in pigs. The amino acid sequence of the FTO gene showed high conservation among human, pig, and other important domestic animals. Twelve variants including ten SNPs and two indels were detected, and then five SNPs within different genomic regions were genotyped in the ISU Berkshire × Yorkshire pig resource family. The linkage disequilibrium analyses revealed that most of these FTO variants were not in strong LD with each other. The SNPs c.46–139A > T within intron 1 and a synonymous mutation c.594C > G (Ala198Ala) within exon 3 had significant (P < 0.01) associations with average daily gain on test and total lipid percentage in muscle, respectively. Five major haplotypes were identified and the subsequent association analyses suggested that haplotype 2 (-CTTGG-) was the most favorable for increased growth rate, while haplotype 1 (-CTACG-) was unfavorably associated with intramuscular fatness traits.     

Y-SNPs Haplotype Diversity in Four Chinese Cattle Breeds

To investigate the genetic diversity of Chinese cattle, 96 male samples of 4 Chinese native cattle breeds were investigated using 5 single nucleotide polymorphisms specific to the bovine Y chromosome. Two previously described haplotypes (taurine Y2 and indicine Y3) were detected in 74 and 22 animals, respectively. The haplotype frequencies varied amongst the four native breeds. The taurine Y2 haplotype dominated in the Qinchuan, Dabieshan, and Yunba breeds. However, the indicine Y3 haplotype occurred in high frequency in the Enshi breed. Among the four native breeds, Yunba had the highest haplotype diversity (0.4330 ± 0.0750), followed by Qinchuan (0.2899 ± 0.1028) and Enshi (0.2222 ± 0.1662), Dabieshan was the least differentiated (0.1079 ± 0.0680). Compared with some foreign cattle breeds, the low level of haplotype diversity was detected in our breeds (0.2633 ± 0.1030).     

An in vivo and in silico analysis of novel variation in TMBIM6 gene affecting cardiopulmonary traits of Indian goats

Transmembrane Bax Inhibitor Motif-containing 6 (TMBIM6) gene acts as calcium leak channel and negatively regulates autophagy and autophagosome formation. The TMBIM6 gene was amplified and searched for variation in three different goat populations (i.e. Black Bengal, Ganjam and Raighar) of Odisha state of the India. The result indicated two substitutions i.e. 55th position (C55T) and 95th position (C95A) in the amplified region of the gene resulting in change of amino acids (Leu > Phe and Thr > Asn). The identified SNPs were combined to form haplotypes and animals were grouped accordingly. Structural analysis showed minor changes (5%) in between mutant and wild TMBIM6 protein structures. However, any functional variation could not be identified with respect to the calcium ligand and open pore state. But an alteration of calcium binding site was found. The binding interaction of calcium with the TMBIM6 protein was hydrophobic in nature in closed state whereas hydrophilic in open pore stage. The stress releasing function was the result of calcium leakage controlled by amino acids coded by exon 4 and exon 5 regions of TMBIM6 gene. The effect of breed and haplotype on cardiopulmonary traits was studied. The data on cardiopulmonary traits of body i.e. rectal temperature, skin temperature, heart rate and respiration rate were recorded when ambient temperature usually remained the highest. The statistical analysis showed, significant difference in rectal temperature, skin temperature and respiration rate among these goat populations. The haplotypes (CC and TA) were found to have a significant (P < 0.05) effect on rectal temperature, skin temperature and respiration rate. However, any such significant effect could not be identified in recorded heart rate. The objective of the present study to identify the genetic variations in TMBIM6 gene having significant effect on cardiopulmonary traits which can be further uses as the molecular markers to improve heat tolerance mechanism in goats.     

Is CD36 gene polymorphism in region encoding lipid-binding domain associated with early onset CAD?

CD36 is a fatty acid translocase in striated muscle cells and cardiomyocytes. Some study suggested that alterations in CD36 gene may be associated with coronary artery disease (CAD) risk. The aim of the current study was to compare the frequency of CD36 variants in region encoding lipid-binding domain in Caucasian patients with early-onset CAD, no-CAD adult controls and neonates. The study group comprised 100 patients with early onset CAD. The genetic control groups were 306 infants and 40 no-CAD adults aged over 70 years. Exons 4, 5 and 6 including fragments of flanking introns were studied using the denaturing high-performance liquid chromatography technique and direct sequencing. Changes detected in analyzed fragment of CD36: IVS3-6 T/C (rs3173798), IVS4-10 G/A (rs3211892), C311T (Thr104Ile, not described so far) in exon 5, G550A (Asp184Asn, rs138897347), C572T (Pro191Leu, rs143150225), G573A (Pro191Pro, rs5956) and A591T (Thr197Thr, rs141680676) in exon 6. No significant differences in the CD36 genotype, allele and haplotype frequencies were found between the three groups. Only borderline differences (p = 0.066) were found between early onset CAD patients and newborns in the frequencies of 591T allele (2.00% vs 0.50%) and CGCGCGT haplotype (2.00% vs 0.50%) with both IVS3-6C and 591T variant alleles. In conclusion, CD36 variants: rs3173798, rs3211892, rs138897347, rs5956, rs143150225 rs141680676 and C311T do not seem to be involved in the risk of early-onset CAD in Caucasian population.     

基于线粒体细胞色素b基因分析海南岛褐家鼠种群遗传多样性

褐家鼠(Rattus norvegicus)是海南岛的主要害鼠之一,海南岛是我国南方海上的重要交通口岸,但关于海南岛褐家鼠的种群遗传多样性以及和邻近地区褐家鼠种群间的基因交流情况还缺乏了解。本研究测序分析了来自海南岛、广东、越南等地91只褐家鼠的细胞色素b基因,分析了不同种群中的Cyt b单倍型,种群间的遗传分化程度(F_(st)),构建了全世界60个褐家鼠的Cyt b单倍型之间的系统进化关系。结果发现,海南岛琼中/澄迈和崖城的褐家鼠种群没有共享的Cyt b单倍型,种群间出现了明显的遗传分化(F_(st)=0.453),但这两个群体分别与广东和菲律宾/越南的褐家鼠分享共同的单倍型,表明海南岛褐家鼠与广东和菲律宾/越南褐家鼠近代存在着基因交流。系统进化分析结果表明,多数海南岛和广东褐家鼠的Cyt b单倍型来自共同的单倍型组CⅢ和CⅦ,说明海南岛和广东省的褐家鼠可能由一个或多个共同的祖先种群扩散而来。由于褐家鼠喜欢与人伴生,褐家鼠很可能随着黎族人在新石器时代中期(大约3 000年前)或更早以前,从广西、广东沿海地区迁移至海南。     

Inversion polymorphism and a new polytene chromosome map of <Emphasis Type="Italic">Zaprionus indianus</Emphasis> Gupta (1970) (Diptera: drosophilidae)

Zaprionus indianus is a recent invader in Brazil and was probably introduced from the West Afrotropical zone. So far, studies regarding its chromosomal polymorphism were limited to India. We found that Brazilian populations were very different from Indian ones. Five new inversions have been discovered. In(II)A, already described in India, where it is quite common, has also been found in Brazil, where it is very rare. The X-chromosome has three inversions; In(X)Na, In(X)Ke and In(X)Eg, which are frequent in all Brazilian populations studied. In every case, we observed strong linkage disequilibrium among these gene arrangements. During the primary collection period (2001–2002), we noticed a significant positive correlation between the frequency of these inversions and latitude, but this was not confirmed in later investigations. Rearrangement In(IV)EF was also common in all populations, while inversion In(V)B was only found in southern populations. Our data suggest that the founders that recently invaded Brazil were polymorphic for the six inversions observed. The place of origin might be identified more precisely by investigating West African populations. In order to facilitate further investigations, we present an updated polytene chromosome photomap, locating the breakpoints of every inversion observed in Brazilian populations. Galina Ananina and Cláudia Rohde contributed equally to this work     

Genetic population structure as indirect measure of dispersal ability in a Lake Tanganyika cichlid

Diversification and speciation processes are influenced by intrinsic (ecological specialization, dispersal) and extrinsic (habitat structure and instability) factors, but the effect of ecological characteristics on dispersal is difficult to assess. This study uses mitochondrial control region sequences to investigate the population structure and demographic history of the endemic Lake Tanganyika cichlid Neolamprologus caudopunctatus with a preference for the rock-sand interface along two stretches of continuous, rocky shoreline, and across a sandy bay representing a potential dispersal barrier. Populations along uninterrupted habitat were not differentiated; whereas, the sandy bay separated two reciprocally monophyletic clades. The split between the two clades between 170,000 and 260,000 years BP coincides with a period of rising water level following a major lowstand, and indicates that clades remained isolated throughout subsequent lake level fluctuations. Low long-term effective population sizes were inferred from modest genetic diversity estimates, and may be due to recent population expansions starting from small population sizes 45,000–60,000 years BP. Comparisons with available data from specialized rock-dwelling species of the␣same area suggest that habitat structure and lake level fluctuations determine phylogeographic patterns on large scales, while fine-scale population structure and demography are modulated by species-specific ecologies.